In recent years, the CGH method has been developed by Kallioniemi, et al. (Patent Literature 1, Non-patent Literature 1). This CGH method can detect copy number abnormality in genomic DNA of whole chromosome in a single hybridization, and has been widely exploited as a method for analyzing genomic aberration. The specific method is as follows. For example, at first, DNA extracted from a tumor tissue (cell) and DNA obtained from a normal tissue (cell) are each labeled with different fluorescent dye (for example, Cy3 and Cy5), and are allowed to hybridize competitively with a normal chromosome sample, and then the difference of fluorescent color of the chromosome is analyzed. In this instance, if amplification of gene/chromosome has occurred in the tumor tissue (cell), a normal chromosomal region corresponding to it will emit the fluorescent color originated from the DNA extracted from the tumor tissue (cell) strongly, because the normal chromosomal region could have hybridized with relatively large amount of DNA extracted from the tumor tissue (cell); on the contrary, when a deleted region of gene/chromosome is present in the tumor tissue (cell), a normal chromosomal region corresponding to it will emit the fluorescent color originated from DNA extracted from the normal tissue (cell) strongly [the fluorescent color originated from the tumor tissue (cell) will be emitted weakly], because the normal chromosomal region could have hybridized with relatively large amount of the DNA extracted from the normal tissue (cell). For this reason, from this hue, the region where the number of copy of the gene/chromosome in tumor tissue (cell) is out of balance can be detected as a position in the chromosome sample.
Furthermore, to perform this CGH method more simply yet quickly, as an alternative to the normal chromosome sample, the CGH microarray method employing a microarray which has been bound with DNA clone and cDNA covering whole chromosome region, oligonucleotide, and the like has been developed (Patent Literature 2, Patent Literature 3, and Patent Literature 4).
However, the above-described CGH method was not necessarily sufficient with respect to detection sensitivity and detection accuracy due to the fluorescent dye to be employed.    Patent Literature 1: JP-A-07-505053    Patent Literature 2: JP-A-2006-9115844    Patent Literature 3: JP-A-2006-94726    Patent Literature 1: JP-A-2005-304481    Non-patent Literature 1: Kallioniemi et al., Science, 258, p. 818-821, 1992.